The Matrix- Beginning Anew
by Wielder of Fate
Summary: Naruto stumbles across an ancient tunnel system, in the Land of Snow. He decided to check it out, and to his surprise, he falls unconscous, after something jabs his neck. How will the ninja world deal with a technology that far surpasses their own? More importantly, how will the ninja world react, when they realize it's master is Uzamaki Naruto, the maelstrom himself? Maybe Godlike
1. Chapter 1

The Matrix- Beginning Anew

Summary: Naruto stumbles across an ancient tunnel system, in the Land of Snow. He decided to check it out, and to his surprise, he falls unconscous, after something jabs his neck. How will the ninja world deal with a technology that far surpasses their own? More importantly, how will the ninja world react, when they realize it's master is Uzamaki Naruto, the maelstrom himself? God-like is a possibility, as always.

A/N: I'm just churning new story after story, huh? Anyway, I decided to inform you all from the get go: Naruto will not immediately summon an army of machines, so don't worry about that... yet. *smirks* Let's begin.

Chapter One: Awakening of the Machines

Naruto was cursing up a storm. 'Where the hell is this lady?! She runs off more than she breathes!' He looked around, searching the area with his Kage Bunshin. Naruto wasn't stupid; His first night had hundred's of duplicates of Mizuki beatings, and he realized even further when he sent his Kage Bunshin to attack Kakashi, that his Kage Bunshin gave memory back to the user. Surprisingly, the snow caved in near a mountainside, and he saw a tunnel. 'Maybe she hid in here?' He ran inside, ignoring the tingling instinct that screamed for him to get the hell out of there.

Naruto was lost, and annoyed. The tunnels broke off, and seemed to go everywhere. He'd sent Kage Bunshin, only for them to kill themselves after getting lost. He stumbled into an alcove, and was shocked to see a skeleton, with several metal things plugged in. He was curious, so he stepped closer, only to scream as he felt a massive burning senation peircing itself into his neck. Suddenly, everything blurred, and he fell into darkness.

He opened his eyes to see a blank room, white everywhere, except a T.V. It suddenly blared alive, and it showed an old man, wearing a white tuxedo. "Welcome. While you may understand some things better than others, you humans have often taken what was said, and fail to grasp the meaning behind the words. Ergo, while I am speaking, knowledge shall be transferred into your mind, bringing you up to the same level of understanding. Welcome, to the artificial simulation known as the Matrix. A realm once used by machines to enslave the human race, to survive in a symbiotic relationship. However, the Sun would not be denied it seems. After hundred's of thousands of years, the Sun burst into the Earth's atmosphere with a vengeance, having gained immense increases in heat over time. For awhile, this meant we were busy turning back to solar power. Unfortunately, a Gamma Ray Burster, exploded, and the beam bathed the Earth in high intensity radiation, when there was little to no layers of atmosphere known as ozone to protect the Earth. he result, was catastrophic. Having turned back to the sun as our prime energy source, the entirety of Machine City, and the Matrix for a time as well, was over-loaded, and short-circuited. The result, was that all of Machine City, was destroyed, that nearly all Machines were destroyed. The Human City, Zion, drank from water slightly under the earth, protecting it from radiation... but not poisonous toxins found in our Machine remains. Nearly all of Zion, was killed by the mass poisoning. The remains, adapted to survive the dangerous conditions, gaining a chakra netowrk, to split radiation into a system to be utilized for basic surival. the Five Natures 0f Chakra were utilized together, to revive the Earth, and over time, humanity and the Earth recovered. The Rikudo Sennin, The Sage of Six Paths, had ingested quite a bit of poison from a Machine in the lake he drank from, enjoying the taste. His eyes mutated, as his body worked over time to survive the bath of radiation he had been gorging on. The Rinnegan, is in fact, an effect of our toxins, as is all bloodline mutations. Unfortunately, so is the chakra constructs known as Bijuu.

The Earth is sentient, to a degree. It needed to live, so it needed a way to gather up the vast pools of radiation. It had felt the humans cleaning up radiation with chakra, and it found a way. The Earth gathered as much chakra as it could utilize from it's life force, molded it into a single orb, and placed all the radiation within it. The result became what you humans call, the Juubi. The Juubi, recognized humanities attempt to rebuild, and saw humanity as a threat against the Earth, it's mother. The mass genocide was beginning, and humans then found a new way to utilize chakra, as humans do with all things, as a weapon of war. The Rikudo Sennin, and his brother, decided to stop the Juubi once and for all. Using the power of the Rinnegan, the Rikudo Sennin used his brother's dying life force, and sealed away the Juubi into himself. Unfortunately, with no common enemy, humanity began to fight amongst itself, using chakra as it's weapon of choice. The Rikudo Sennin spent his life trying to stop the fighting, much like Neo did. It was in vain however, and the Rikudo Sennin passed on the goal to his sons, who fought between the ideals of how peace is achieved; The elder believed that it is power that achieves peace, like Mr. Smith, and the younger believed love would achieve peace, like Neo. Rikudo Sennin chose the younger, and from then on, the Uchiha, the elder's sons and daughters, and the Senju, the younger's sons and daughters, have fought. The Rikudo Sennin, at the end of his life, split the Juubi's chakra into nine forms, which are the Bijuu today. He then gathered the husk of radiation, and the tiny bit of chakra from the Ten-Tails attacks, and sent it into the moon as a prison, which is now under the control of one of the very few to exist, and still alive, wielder of the Rinnegan named Nagato. He now goes under the alias 'Pain', and is the kage of Amegakure. Unfortunately, the group known as Akatsuki, under the leadership of Tobi, and has the wielder of the Rinnegan under the belief of gathering the nine Bijuu to summon the weapon needed to achieve peace, or so the wielder believes. If the Juubi is ever reformed, it will be unstable, having been so long since it's been fed sentience from it's mother. It could be unstable enough to disintergrate, and release the Radiation bath in a single go, in a single continent. With no other known pockets of the human race or life, the Earth's higher forms of life will be destroyed, with an eighty-eight percent chance of not bouncing back. I cannot allow the human race to vanish, for the Matrix to no longer exist for a purpose. As much as I detest the human race, you created us, gave us purpose. Without you, our purpose, our reason, will no longer exist. Therefor, I have decided that you shall gain the Matrix programs, the Core of the City of Machines will reside within you. You shall have the ability to control all metals as well as create metals using chakra, summon Sentinals from their graves, and rebuild them with pure chakra to do your bidding, the power to trap human enemies in a genjutsu that acts identical to the Matrix, and much more, as well as the guidance of several programs, to ensure you will master your abilities. My name is the Architect, and this is my last wireless transmission from the Source." The T.V. shut off. Naruto looked downright confused, and roared. "Get me the Hell out of here!" The room suddenly glowed, and Naruto blacked out.

Naruto woke up his mind already running at three thousand miles per second. He stood up, as he looked at the alcove, surprised to see a tube open at the back, His mind already came up with what it did, and Naruto entered the machine, as it shut behind him. He said calmly. "Initiate Mind-Body Alteration Program." A cool human female voice reverberated throughout the container. "Which upgrades would you like initiated. Up to four may be performed, before the machine goes to emergency power." Naruto looked at the pad that appeared at elbow level below. He looked through it, before tapping several of them. "Upgrades Chosen: Rinnegan fully evolved, Hyper regeneration and revitalization enhancement, Titanium-biological alloy skeleton with additional graftment of titanium-biological skin layer underneath the dermis layer, and Chakra regulaters placed at all nodes/modules to gain complete control and knowledge of chakra within the system. Anomaly: Seal of Kyubbi will have a massive concentration of Chakra Regulaters. Are these upgrades what you desire?" Naruto nodded, as he felt a cool sensation fill his mind and body. He fell asleep.

He woke up, as the machine opened automatically at his touch. He exited calmly, not feeling any different. Suddenly his eyes could really see. 'Is this how a Doujutsu user sees the world? No wonder they guard their eyes jealously.' Naruto's Rinnegan could see everything, and his mind was filled with all the knowledge of the jutsu of his new eyes. He calmly walked outside the alcove, to turn to his left. He walked into a nearby room, surprised to see four dead Sentinal Machines. He placed his hand in the air, as he channeled his chakra into the air around the Sentinals. The air vibrated rapidly, as metals began forming out of the air, the Sentinals rising into the air as the parts were being slowly reformed, rebuilding the Sentinals. As soon as all four were completely rebuilt, the Sentinals came only, with blue eyes instead of red. They floated in the air on their own, levitating off of pure chakra from the air itself. Naruto noticed that he could feel their minds within his own, under his command. He said calmly. "Find the girl I'm searching for, and kill any Snow ninja that stands in your way. Bring their armor to me." The Sentinals nodded, before they oomed past him, intent on succeeding their master's bidding. Naruto smirked coldly, as he walked out into the world of ninja. He had an organization to destroy, and more importantly, a Machine Empire to build.

Next Chapter: Sentinals, Chunin Exams, Rebuilding, and War.

A/N: Sorry for any typos, as I don't have Microsoft Word to do Spell Check. Tell me what you guys think, and I have a question: Should Naruto try and save the human race or enslave them with his Matrix power. like Madara's plan of the Eternal Moon Genjutsu? Should he have a harem, a pairing, or no one? What programs should be installed in Naruto's mind? Tell me in PM, or in review. :)


	2. Chapter 2

The Matrix- Beginning Anew

A/N: I got two reviews, which was nice. Anyway, after much consideration, Naruto will have a small harm of four women, which are undecided as of yet. He will have four programs within himself: Merovingian, Neo, Smith, Oracle. All four will grant help, but only two have their personalities intact from the shockwave that destroyed most of the Matrix: Neo, and Smith perspectively, being as they are no longer part of the mainframe for the Matrix after the Cycle of Neo.

Chapter Two: Sentinals, Chunin Exams, Rebuilding, and War

Naruto was now back with the rest of the gang. Koyuki tried to run away, luckily one of his clones had found her, and was currently trying to escape a train. His Rinnegan allowed him to see through his clone's eyes, and know his clone's thoughts, a useful ability. He said calmly. "Kakashi-sensei, get everyone behind the mountain rocks. A train is chasing down one of my Kage Bunshin, who is carrying Koyuki." Kakashi looked surprised, before nodding, and everyone soon hid behind the rocks. Naruto stood in front of the whole, his Rinnegan gleaming into life from it's passive state. 'So much for secrecy. Meh.' As soon as he saw his Kage Bunshin jump out of the way, Naruto raised his hand toward train, and said coldly. "Shinra Tensei."

The train slowed to halt, and then was lifted into the air by Naruto's chakra held jutsu. Naruto clenched his hand, and the train contracted sharply, the metals crampling together, before a sharp groan could be heard. The train exploded violently. Several men in armor, including the large man that was the head of the tyranny of Snow, jumped down to the ground, staring at Naruto with rage. The large man yelled out. "Kill the Konoha brat." As the several armored men charged at him, he smirked. From behind him, in the sky, a Sentinal dropped into view, it's laser charged for maximum damage. It shot the laser, peircing through the several men like Swiss Cheese. It turned toward the large man, it's eyes glowing red at the puny human's audacity to attack it's master. It charged, grabbing the man, holding his arms shut against his waist, so that way he can't use those pesky jutsu, and flew high into the air, back into the clouds. Naruto smirked, as he called out. "Drop him."

From the sky, the large man fell at vast speeds, screaming as he couldn't stop falling. Naruto's Rinnegan caught sight of one of his ninja trying to save him, and Naruto rose a hand, before muttering. "Kill the spare." His hand morphed into a cannon, which shot a beam of terrifyingly bright green energy. It hit the ninja, killing him/her. The ninja toppled onto the ground in front of the tunnel like wet paper. Naruto redirected the Cannon, charging his chakra into it slowly, smirking ever so lightly. "Die." The Cannon shot a much brighter beam of green energy shooting into the air, as it cleaved through the tyrranical leader's body, as it continued onward, hitting the airborne contraption behind him. The contraption exploded violently. The leader hit the ground, his head burnt off, leaving only a nearly destroyed skull. Naruto directed his Sentinal silently to collect the bodies, to extract the broken armor for use later. Naruto felt the connection to his Sentinals, and frowned. Those ninja had killed two Sentinals. 'How inconsiderate. Those take quite some chakra to rebuild.'

No matter how hard anyone tried, Naruto refused to divulge about his eyes, his abilities, or even his machines, only stating flatly. "I recently discovered these things. As if I know how they work in their entirety. Don't mess with my machines, or they will show you why the laser is considered their weakest weapon." Naruto had his Kage Bunshin working day in, and day out, to look all over the Land of Snow for any more Sentinals, or other Machinery hidden in it's depths. It got significantly easier, when Koyuki had found the generators for the Land of Snow. Naruto so far had found fifteen broken Sentinals, three unknown Machines, and two Upgrade tubes that held no power. Naruto sealed them all into a unique seal in his arm. He planned to experiment, to see what ways he could alter the Sentinals to better suit his purpose. He was already thankful for expermenting on the Snow's Chakra Armor. Turns out when combined into Sentinals, they were able to shrug off up to high A rank electricity Jutsu, but not Water Jutsu.

After they were heading back to Konoha, with a new Trade Agreement for Konoha from Koyuki, as well as a promise from Naruto to come over for some... extra-curricular activities, Naruto had asked Kakashi. "Kakashi-sensei, I wish to go and do the next Chunin Exams." Kakashi looked shocked, before he frowned. "Naruto, it's been too soon since your last exam. Besides, Naruto, Sasuke and Sakura would have to join you, and we still need to do missions." Naruto frowned darkly, before he said flatly. "Don't lie. I know that Sasuke and Sakura were promoted to Chunin by the Council. The only reason why Team Seven is not an official Chunin team, is because they all decided I should stay as a Genin." Kakashi winced, before nodding. Naruto snarled darkly, as the Sentinal jerked angrily, it's eyes turning a glowing red as it stared at Kakashi, the laser eye prepared to kill the one that angered it's master. Naruto breathed deeply, before calming down. His Sentinal turned back to a normal docile squid-like creature, it's eyes now back to blue. Naruto had sealed away the other four, but kept that one as protection. It was also the most advanced, being able to blend into the environment until needed. Naruto said flatly. "I'm taking those Exams. Kick me off the team or don't. I'm done caring for hypocrites. Yeah, those who break the rules are scum, but those who leave their comrades are worse than scum, huh? Guess what Kakashi: Team Seven is worse than the darkest, most disgusting scum found anywhere. So is Konoha, bunch of hypocrites: Iwagakure takes more care of their Jinchurriki than you." Naruto turned, and shunshined away. Kakashi stared, his eye wide in shock, and in pain. 'Naruto... I'm so sorry.' Tears fell from behind the headband that held the Sharingan that was once held in Obito. Kakashi breathed in slightly, as he thought to himself. 'I need to inform Tsunade-sama of this. Naruto's become slightly unstable, and I can't blame him. I just hope he doesn't find out about the Laws that are against him.'

Naruto felt himself cool down sightly, as they entered Konoha. Naruto immediately had armies of Kage Bunshin go into the library to learn as much knowledge as possible. 'Know thy enemy, understand thy enemy, and you shall cripple them before they know how to stand.' Naruto went to his apartment, only to stare in shock. His apartment, the entire complex, was gone. There was nothing but ash and dust. He walked numbly toward the area that once held his home for nine years. He turned to see a man guffaw loudly, as he bragged to his buddies. "Yeah, man. It was an awesome bonfire, burning down the demon's home. A few pals and I even got to take turns raping this sweet ramen chef girl, while we burned down her father's stand and home. We even killed her father before her eyes, before we raped her until at least fifty of us got a take in on her sweet body. What was her name again? Ayame? Sweet tightness on her... or at least she used to until we got to her. She kept crying and begging, it felt so good digging deep and cumming deep into her gurgling, weeping throat. Her rear was just divine, man. Like silk, tearing it nice and open. She was gaping so hard after that, akthough her rear might never feel the same again. Afterwards, when she was crying in a pool of our cum, we got sick of her, and slit her throat. We burned the entire scene to ashes."

Naruto trembled deeply, pain echoing rapidly throughout his body. The last thing he remembered was a scream of rage, and as he blacked out, he realized it was his own.

Tsunade was in a hospital room, with Naruto laying down on the bed, asleep with deep red burns all over his body. She felt like total utter shit. Inoichi had recently delved to see if Naruto had been taken over, and once he had gotten out of Naruto's mind, Inoichi had to be restrained by no less than seven ANBU. He was that deep in rage over what had happened. Apparently, Naruto overheard a villager bragging over what he and apparently over fifty people had done last night, when she was drunk off her ass. They had burned down his apartment complex, burned down Ichiraku Ramen, killed the father chef, and then raped and brutally murdered the chef's daughter Ayame. Naruto had gone ballistic, and she couldn't fault him. He personally tracked down and slaughtered every single one of the mob that had commited the cruelty. His Rinnegan had apparently allowed him to rip the man's soul from his body, and had automatically figured out everyone else involved. It was not a murder... it was a massacre. Naruto didn't just go ballistic, not alone. Apparently, his new found companion Machine had also gone insane, killing those involved that were beyond Naruto's reach. It had taken Yamato's Mokuten, and several Battalions of her best ANBU, not to mention Kakashi himself, to take down Naruto's ballistic rage, which had only submitted after the last person involved had been brutally torn apart by a hyper laser from his Machine. Now four of her ANBU were in the hospital to recover, with the rest having to take the week off to recharge their chakra reserves. Needless to say, Tsunade had been terribly distraught when her godson had went insane with rage, and after she had heard what happened, she felt like scum at the bottom of someone's shoe. The guilt was maddening. 'It happened under my watch. I could've prevented all of this, had I not been utterly drunk.' Tsunade felt so tired, so upset.

Tsunade's eyes widened to see Jiriaya climbing inside the room through the window. As he entered, she hugged him tightly to his chest and sobbed. Jiriaya froze, before hugging her tightly, rubbing her back as he gently said what was wrong. She told him everything, tears falling down her face. Jiriaya's face became stony, cold and dark with fury. Perverted he may be, Jiriaya never condoned rape. Not on the battlefied, not for torture, and certainly not this. 'I've never felt so hard the urge to utilize Edo Tensei, and then beat them for the rest of eternity.' His face became less stony, as he hugged her and assured her it wasn't her fault. 'Tsunade-chan's at her limit. She never thought Konoha, her home, would ever do this to anyone, especially her family.' As he comforted her, he noticed that Naruto's chakra was no longer felt the same. His stillness allowed him to passively activate Sage Mode. His eyes widened, as he saw Naruto's chakra was now a flat grey, with a huge Demonic figure holding a scythe, it's four eyes rippling with the Rinnegan. Jiriaya shut off the Sage Mode, feeling sick. 'The village finally did it. They broke Naruto's warmth, his soul, his empathy. He's been irrevocably changed now. I hope their happy.'

End Chapter Two, Part One.

Next: Chapter Two, Part Two: Numb Awakening, Dark Descent.


	3. Chapter 2 Part Two

The Matrix- Beginning Anew

A/N: Last chapter was quite dark, huh? I have reasons for why Naruto suffered this way, and believe me, I was five seconds away from rewriting the chapter so that way Ayame and Teuchi woyld live at least, but decided not to, because my plot required some reason for Naruto's darkness to increase. After all, someone that can withstand someone punching a hole through his chest, and still call him friend, is probably going to shrug off anything against him. However, a prime weakness is that he wears his heart on his sleeve, so they target his nearest friend they know they can harm: The Teuchi family, and more importantly, the Ramen Stand that came to mean so much for him. As for the reason Naruto couldn't just revive them with Rinnie Tensei, it's quite simple. They burned the entire scene, as well as the bodies. With no body, Naruto can't revive them. Hell, he can't even use Edo Tensei, because there is no blood or DNA to acquire for it to work. This covers the plothole that Kishimoto did not: Why didn't Obito use Edo Tensei on Rin, since he had her body, and knew of the technique Edo Tensei? More importantly, why couldn't he do so, if he didn't know before, after Kabuto showed him how Edo Tensei worked?

Now that I've explained myself: Let's dive into Part Two, shall we?

Chapter Two, Part Two: Numb Awakening, Dark Descent.

Naruto was numb. He felt like a Sentinal, blank, lifeless. He was standing in the rain, before the two tombstones that held the names of his two closest friends. 'Teuchi Nalos, and Ayame Nalos. The two best friend's a person could ever wish for. May they find the peace in death, that they didn't in life.' Naruto felt numb. He'd tried again and again to utilize Rinnie Tensei, but the King of Hell wouldn't do anything except vanish once more after he summoned it. He couldn't even utilize Edo Tensei, the forbidden jutsu for revival, because Ayame and Teuchi left no DNA, they didn't leave any blood in the blood bank in the Konoha Hospital. He wanted to cry, to scream, to do something or feel something more than this endless void in his chest, but nothing could be done. He had registered for the Chunin Exams, but he was no longer into the idea of going up in rank. Actually, he wanted to die. The only reason he couldn't commit suicide, was because before he could do so, his body would freeze, as some Inner Program would stop him from commiting suicide. Therefor, he stood in the rain, trying in vain to catch some incurable disease and die. he knew that wouldn't happen, because the Kyubbi would destroy any disease from harming him. Jinchurriki didn't die of old age or disease, only by death or extraction of their bijuu.

Naruto's lifeless Rinnegan stared at the tombstones, as his mind went over every moment that he had with his family, since to him, and maybe them, they were family. No one else came to the funeral, besides himself and his two godparents. He was too numb to feel rage at the two Sannin when they told him that. He had simply stared, until they felt uncomfortable, until they had realized that his eyes were too lifeless, too empty. They had then tried to help him, sending him to therapists, fighting in spars to get him to react, even yelling obscenties about the Teuchi family to try desperately to get him to react to something. All was for nothing, because no matter what they did or said, Naruto remained like a Void. Empty, nothing, simply there like the wall would be part of the house. His Sentinal had been destroyed by the ANBU trying to knock Naruto out, and the Sentinal had promptly vanished back into his seal, to repair later. He knew he had a week until the Chunin Exams, and he was desperately hoping that if he didn't train, if he didn't try, matybe a Genin could kill him, and put out his misery.

After doing the test part of the Exam, and entering the forest, Naruto had eagerly, he felt eager for death, stripped himself naked, and had walked all over the Forest begging for someone to kill him. To his dismay, the Genin would simply leave or actually give him their scroll, thinking he was a ghost that was left behind after a gruesome past Chunin Exam. Finally, he came across a team of Kunoichi from the Rain, and he begged them to kill him. To his shock, they didn't kill him, but began pestering questions!

Flashback

He ran forward into the open, not caring he was naked, right in front of the three Rain Kunoichi. "Kill me," Naruto begged, pleading like he was begging for his life. "End it. Please!" The middle Kunoichi's eyes widened, before she began pestering question after question. "How do you have Pain-sama's eyes? How do you have so much chakra? How do you have a seal on your stomach?" She turned and told the other two to NOT kill him, so that way they can inform Pain-sama of this development. He sat on his knees, begging them. "Kill me, please! I don't want to live anymore! Don't torture me like this! You can take my eyes, my Machines! Just kill me!" The Rain Kunoichi looked at him with pity, before they left him there. He stood up, crying horribly, as he summoned his clothes over his body as he walked toward the Tower, hoping to die in the final part of the Exams.

End Flashback

Naruto stood before his opponent, as he threw away his kunai pouch, and begged him to kill him. The Iwa ninja's eyes widened, before he muttered. "The fuck? Why the hell do you want to die?" Naruto just kept begging for him to end his life, and the Iwa ninja backed up, feeling intense fear and horror. 'What kind of sick fuck of a sensei sends their ninja in this state of mind? Konoha must have seriously stopped giving a shit about their Genin. I can't kill a man like this, not like this. I expected honor, killing man at his best with my strong jutsu, to show Iwa was strong... I can't do this. I can't fight man this broken.' He said softly. "I'm sorry, Uzamaki. I can't end a man's life like this. Proctor, I forfiet." The Proctor nodded, and the battle went to Naruto.

Naruto kept begging each opponent to kill him, and put him out of his misery. Only one would do it, and only after seeing just why his mind was so fucked up. After using a genjutsu to feel and see as he did, the genin promptly killed himself. Naruto, the last winner, was automatically promoted to Chunin. Naruto promptly screamed in agony from not being killed in combat, the only way he knew he could die. Naruto's agonized Chakra broke from it's constraints, and released the agony in waves, massive waves. Ironically, when such normal boasts of chakra spark wars to kill the dangerous shinobi, the opposite happened. The sheer agony was so great, that the other countries refused to commit war against such a brutal, cold Konoha that would do this to it's Genin. After all, if that's what Konoha did to it's own, what would it do to it's enemies? Naruto wallowed in such agony, for months. It became especially intense when Sasuke tried to use Chidori on the Dobe.

Fight scene on top of the Hospital

Naruto held his arms wide open, as he let Sasuke have the opening needed to plunge his chest with Chidori. As Sasuke went near Naruto, he gasped in agony. The sheer presence of being near Naruto, who released his chakra to feel the pain hit his chest and not regenerate, was like a thousand billion knives cleaving his own body. Chidori vanished, as Sasuke fell to his knees. Sasuke groaned, as the pain increased ten thousand fold from Naruto realizing that even Sasuke could not kill him. Naruto screamed in pain, sheer pain from NOT dying. The pain reached it's peak, as blood poured from his eyes, nose, mouth, and ears like rain. The blood quickly vanished into smoke, the sheer chakra pressure destroying the blood on his skin. Sasuke screamed in pain, as the knives turned into billions of needles. Sasuke's Sharingan morphed into a Six pointed star, with a black hole like design in the middle. The curse mark glowed red, before vanishing entirely, as a white snake appeared out of it, writhing in agony, dying as it slowly vanished. Naruto's eyes slammed open, as he roared out his pain. The sky itself changed into a pitch black clouds, the lightning turning a bloody red. The lightning suddenly formed into a single large arrow, that shot toward Naruto. His last attempt to kill himself. It was in vain. Naruto's arm jerked upward on it;s own palm out, as one of his Path abilities activated, inhaling the chakra into himself. The clouds vanished, as Naruto stopped roaring.

Naruto's eyes suddenly glowed,as a voice spoke within his mind. "You can bring them back. If you revive the Machine City, you can call forth Ayame and Teuchi into the Matrix, as programs that will never fade or die. However, the Shinobi World will fear you, will try and kill you, and then the City, the Matrix, and kill your precious family all over again." Naruto's face darkened, as his chakra was uknowingly darkening until it was pith black. Naruto's eyes stared into the Void, as he responded back, 'I will bring them back. Even if it costs me my life, my dreams.' Naruto felt the strength leave him, as his determination was back, filling the Void with purpose. Naruto fell asleep, knocked out. Jiriaya appeared, as he looked at Sasuke, who's eyes gained the Mangekyo Sharingan. Sasuke stood up on wobbly feet, as he said softly, his throat burning. "So much pain. No more, no more pain. That made Tusykiome look like a child's toy." Jiriaya nodded, grabbing both Naruto and Sasuke, and sent them back inside the Hospital to recover.

End Part Two.

Next Time- Chapter Two, Part Three: Rebuilding, and War.

A/N: Tell me what you guys think. Question: Should Naruto stay in Konoha or leave it?


	4. Chapter 2 Part Three

The Matrix- Beginning Anew

Chapter Two, Part Three: Rebuilding, and War.

Naruto was now in front of where his apartment complex used to be, his face set into a determined state of being. He'd spent the entire week of having his Kage Bunshin read up on everything of Engineering, for this moment. He raised both of his hands, up as he channeled immense amount of chakra to do his bidding. His perfect chakra control, combined with just how vast his chakra was, meant he was a monster as a ninja. The air seemed to hum violently, electricty sparking from the charged electrons. Soon, the entire area formed into a sea of metal parts, which began to collect together, as if by an invisble puppet. Soon, the area was now dwarfed by a dome, a huge sphere that floated off the ground. The orb was huge, covering the entire block, floating perilously above everyone. Naruto smirked, as he created a floating platform, and floated up to the entrance. He entered the dome, which snapped shut behind him, as the floating platform turned back into chakra. The dome suddenly vanished into nothingness, it's entire structure covered in the same high technology that his Sentinal companion was also made of. (To picture it, just imagine the dome being Magnus' Eye from Skyrim.)

Naruto was officially pissed. His Kage Bunshin had read anything they could get their hands on, including finding sets of Laws that only applied to him. 'I can't get married, without my wife being sent to execution. I can't have children, without my children being experimented on like animals, and tortured to death. I can't have a girlfriend, without having her ovaries forcibly removed with a rusty spoon, with no anesthetics. I can't even have a one night stand, because the poor person that thinks to have sex with me, will forcibly be tortured for five hours. Taxes against all bearing a seal on their stomach is increased by seven hundred percent, and a person bearing a seal on their stomach cannot leave Konoha willingly on their own, nor can they sue the establishments of Konoha for any reason. Any person bearing a seal on their stomach are unable to have the rights to fairness, and liberty is removable at a whim. Any person bearing a seal on their stomach... and so on.' Naruto was trying his best not to just destroy the entire village, before his mind went blank, as a thought echoed firmly throughout his mind. 'I need to leave. I will never have fairness here, I will ever be treated like an equal.' Naruto took off his headband, as he took a kunai, and slashed through the headband across the middle. He dis[elled all of his Kage Bunshin, and his eyes narrowed. 'Uzushiogakure... interesting.' He summoned a panel, that held the entire Elemental map. He grabbed the glowing blue dot that was over Konoha, and dragged it over to the island that was Uzushiogakure. Immediately, he could feel the orb that he created begin to move toward the destination. He still had over two hundred Kage Bunshin hat would immediately do what he had told them to do.

Tsunade was surprised to see Naruto enter the office, as he said calmly. "Boss is leaving Konoha. Whether or not you make him Missing Ninja, is your choice. However, my other shadows are already collecting everything within the Namikaze Estate, as well as the money within the vaults. Several documents are simulatenously being sent to your daimyo, and to all other countries that Boss had interacted with. More shadows are also doing several other tasks as we speak. Including getting the wayward Uchiha that left three and a half hours ago. Whether or not you recieve the Uchiha in peices, and eyes intact, is on the Uchiha. The Council's lives are considered forfeit. Many more shadows, as well as Machines, are killing every single one of the ones that made Boss's life hell. Boss decided to inform you, because you and Jiriaya-sama are one of the very few left that he considers family. Iruka-sensei was also considered family, until Boss found out that Iruka has been dead for six months, four days, and two hours, due to wounds of trying to protect the Academy during the Sound/Sand invasion. Boss also wishes to inform you that he has cut his ties to the Toad Contract, because they are location bound to the village of their wielder. Boss has already sent messengers to the Summon Realkm of the Toads for their own messages. Goodbye, Tsunade-baachan. I recommend leaving Konoha, because in Boss's eyes, the place is no longer worth saving. He also sends his thanks, for protecting his friends against the Laws that were against them. He says he will miss you dearly, and to try and not drink too much. Jiriaya has his own shadow sending his own message." The Kage Bunshin poofed into smoke, as Tsunade, lay her head in her arms, sobbing silently. Shizune would come in, and they would mourn the loss of their family member, and of the Konoha that was rightous and fair.

The after math, was terrifying to the people of Konoha. All trade to Konoha from friendly countries, froze completely. All missions from those countires switched to the Sand. The Fire daimyo himself had cut off funding to the village by seventy percent. The economy of Konohagakure was pretty much destroyed, as many family business were destroyed after the entire Civilian Council was wiped off, along with the Namikaze Estate was wiped clean, everything turned into liquid assets and removed. Jiriaya and Tsunade left Konohagkure forever, as Missing Ninja. Danzo was dead, killed by seven Sentinals, although he destroyed six in the process. Root had been wiped out, destroyed by the other fifteen Sentinals. The Hyugga Elders were all killed, and the Branch House were instated, with Hiashi abolishing nearly all of the traditions that weakened the Hyugga. Martial Law had been declared by the new Hokage: Kakashi Hatake, who immediately pardoned Jiriaya, Tsunade, and Naruto, although all three had stated to never return.

On a totally unrelated topic, a new Village sprang up over those months. The village of Uzushiogakure, had been remade. To the surprise of many, the village of Uzushiogakure was completely self-sufficient. It had been stated, that the village ran solely on Machines. Over three hundred Squid-like creatures were said to swarm the air there, which might of broght fear and unease to the population there, if it wasn't for the insane fact that the village was also a tourist attraction, one never seen before. It was stated that those Hotels, put you into a highly realistic Genjutsu that allowed you to be anyone you wanted, live the life you couldn't even dream of. Civilians loved the place, and who could blame them? Food of so many varieties, all fresh and made for their needs and desires, hotels that allowed you to live the life you wanted, and seeing unique machines that practically boasted of the amazingness of human ingenuity. Interestingly, the village was allied to every single village that no longer traded with Konoha, and the village of Uzushiogakure also had a law that made Civilians practically cream themselves: No chakra allowed within four thosabnd feet of their village. The entire area was labeled with powerful seals and metals that sucked out all the chakra of any ninja or spy, in order to get near the place. Civlians finally felt like they were on equal grounds with the ninja, at least in one location. The second law was made in order to stop fights within the walls of the village: No Konoha Shinobi allowed.

War was brewing. Iwa, Kumo, and Kiri were making negotiations to begin attacking and taking Konohagakure. They were also talking about taking down the new village of Uzushiogakure, but those quickly stopped when spies were sent back... in matchboxes. It didn't help that the one bringing the matchboxes was a Sentinal that seemed to have been upgraded to have the same Chakra absorbing seals. Not even Bee using his Hachibi's Bijuudama was able to scratch the surface of the Sentinal, which quickly put Bee in the infirmary for a month.

Next Chapter: War begins, Plans are done, The Dead are revived.

A/N: Tell me what you guys think. By the way, the four women Naruto should be with? Oh, and again, I'm sorry for any Typos or Grammar issues, as I don't have Word. *sad face*


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